Merge pull request #489 from szilvajuhos/master

Adding exception handling to ASCAT when it is not able to find optimum
SciLifeLab · Oct 27, 2017 · 2b0d7f5 · 2b0d7f5
2 parents 0d7fc10 + e3d7141
commit 2b0d7f5
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/bin/run_ascat.r b/bin/run_ascat.r
@@ -43,6 +43,12 @@ cnvs=ascat.output$segments[ascat.output$segments[,"nMajor"]!=1 | ascat.output$se
 write.table(cnvs, file=paste(tumorname,".cnvs.txt",sep=""), sep="\t", quote=F, row.names=F, col.names=T)
 
 #Write out purity and ploidy info
-summary <- matrix(c(ascat.output$aberrantcellfraction, ascat.output$ploidy), ncol=2, byrow=TRUE)
+summary <- tryCatch({
+		matrix(c(ascat.output$aberrantcellfraction, ascat.output$ploidy), ncol=2, byrow=TRUE)}, error = function(err) {
+			# error handler picks up where error was generated
+			print(paste("Could not find optimal solution:  ",err))
+			return(matrix(c(0,0),nrow=1,ncol=2,byrow = TRUE))
+		}
+)
 colnames(summary) <- c("AberrantCellFraction","Ploidy")
 write.table(summary, file=paste(tumorname,".purityploidy.txt",sep=""), sep="\t", quote=F, row.names=F, col.names=T)
diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config
@@ -33,10 +33,10 @@ process {
   $RealignerTargetCreator.container   = "${params.containerPath}/gatk-${params.tag}.img"
   $RecalibrateBam.container           = "${params.containerPath}/gatk-${params.tag}.img"
   $RunAlleleCount.container           = "${params.containerPath}/runallelecount-${params.tag}.img"
-  $RunAscat.container                 = "${params.containerPath}/r-params.base-${params.tag}.img"
+  $RunAscat.container                 = "${params.containerPath}/r-base-${params.tag}.img"
   $RunBamQC.container                 = "${params.containerPath}/qualimap-${params.tag}.img"
   $RunBcftoolsStats.container         = "${params.containerPath}/caw-${params.tag}.img"
-  $RunConvertAlleleCounts.container   = "${params.containerPath}/r-params.base-${params.tag}.img"
+  $RunConvertAlleleCounts.container   = "${params.containerPath}/r-base-${params.tag}.img"
   $RunFastQC.container                = "${params.containerPath}/fastqc-${params.tag}.img"
   $RunFreeBayes.container             = "${params.containerPath}/freebayes-${params.tag}.img"
   $RunGenotypeGVCFs.container         = "${params.containerPath}/gatk-${params.tag}.img"